Is there a way to limit the amount of penalties through gameplanning?

Get higher Intelligence / Discipline Players

my worst offender has 68 INT and 92 DISC, as well as 86 RBLK and 100 PBLK.

Please post a player/team link so I can have a better idea. But meanwhile
In my opinion, which I am sure others will disagree just because
The higher INT/DIS ratio, the least likely of a penalty.

RB/PB has no reason here
You claim a 17/23 ratio
That's a 26.0% chance of committing a penalty (a/b - 1) Do the math and see if I am correct

Chance of committing Penalty / plays ran

https://paydirt.myfootballnow.com/player/1110

Here is the worst offender.

so a player with an Intelligence of 60 and a Discipline of 30 would commit less penalties?
(a/b-1)

DI is supposed to reduce penalties, but I don't believe it. I started weighting it as a Secondary Non-Improvable skill in my weights, and I'm still one of the most penalized teams in my leagues. Penalties are too much the product of the RNG.

In my experience there seems to be very little to no correlation between high Dis and Int and the amount of penalties called on a player.

I used to put a huge emphasis on discipline 'cause I hate penalties, only to still watch my teams consistently lead the league in penalties. The o-line especially is egregious in this regard, with near constant false starts and holding calls, even when playing obscenely awful d-linemen.

Me too. Now I pretty much ignore discipline, and I have noticed no difference in penalties whatsoever (or anything else).